Main resources (click the image to go to the website)
Interdisciplinary Computing and Complex Biosystems (ICOS) research group. School of Computing Science Newcastle University. Members of the Centre for Synthetic Biology and the BioeconomyAGM - PI/Academic
Synthetic Biology Open Language (SBOL). Representation of genetic designs through a standardised digital format. Visit also SynBioHub - a design repository for people designing biological constructs. AGM - Editor

Standard European Vector Architecture (SEVA). D
atabase and material repository of standard and modular plasmid vectors for (de/re) constructing complex bacterial phenotypesAGM - Contributor

CellShape: an image analysis tool for fluorescence microscopy images. Sub-pixel precision. Quantification of bacterial factories inside. The image links to the code site. (Go to the publication). AGM - Developer


The software DiSCUS (Discrete Simulation of Conjugation Using Springs) is designed to simulate bacterial growth and communication through horizontal gene transfer (conjugation). The software (v1 - released 2012) can be downloaded from here. DiSCUS paper, which explains parameters and dynamics can be found here. Demo videos:

Demo Dynamics - 2‎

Demo Dynamics - 1‎

Demo Conjugation - 1

Demo Conjugation - 2